DNMTs repress unmethylated gene? - (Apr/29/2005 )
Hi, guys. I have a gene which is methylated and thus downregulated in many cell lines but unmethylated and also downregulated in HCT116. The treatment of 5-aza, TSA and both of HCT116 didn't have any effects on its expression. (The result of treatment was confirmed by another gene). However, here is the problem. The expression of the gene was increased at least 5-fold in HCT116 DNMT 1KO, 3BKO or DKO cells. So I don't know how to explain and what mechanisms are underlaid? Did any expert have the similar experience? Any suggestions? What to do next?
Thanks a lot in advance.
Hello,
Maybe in your case it's too early to conclude that DNMTs can repress gene transcription independent of DNA methylation although such possibility exists. Once DNMT binds to DNA, it can recruit other enzymes such as HDACs to repress genes.
How big a region on the promoter have you mapped for methylation and by what method, MSP or sequencing? It could be some area further upstream or downstream that is methylated and silences the gene.
it could also be that knockout of DNMT reactivates other gene through demethylation which subsequently activates the unmethylated gene through some other pathways.
Hope that make sense.
Maybe in your case it's too early to conclude that DNMTs can repress gene transcription independent of DNA methylation although such possibility exists. Once DNMT binds to DNA, it can recruit other enzymes such as HDACs to repress genes.
>Yes. You are right. Thanks. But the TSA treatment didn't have effects on its expression.
How big a region on the promoter have you mapped for methylation and by what method, MSP or sequencing? It could be some area further upstream or downstream that is methylated and silences the gene.
>The regulatory system of this gene seems have nothing to do with its methylation status, because it was not responsive to Aza treatment.
it could also be that knockout of DNMT reactivates other gene through demethylation which subsequently activates the unmethylated gene through some other pathways.
>Correct. But if it is the case, Aza treatment should also have some effects on its expression.
Hope that make sense.
>Thank you very much for you quick response. Good week end and holiday!